R语言 CSAR包 permutatedWinScores()函数中文帮助文档(中英文对照)

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permutatedWinScores(CSAR)
permutatedWinScores()所属R语言包：CSAR

                                         Calculate scores for permutated read-enriched regions
                                         计算分数为permutated读丰富的区域

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Calculate scores for permutated read-enriched regions
计算分数为permutated读丰富的区域


用法----------Usage----------


permutatedWinScores(nn = 1, control, sample, fileOutput, chr = c("chr1", "chr2", "chr3", "chr4", "chr5"), chrL = "TAIR9", w = 300L, considerStrand = "Minimum", uniquelyMapped = TRUE, uniquePosition = FALSE, norm = 3 * 10^9, backg = -1, t = 1, g = 100,times=1e6,digits=2,test="Ratio")



参数----------Arguments----------

参数：nn
ID to identify each permutation
ID来标识每个置换


参数：control
data.frame structure obtained by loading the mapped reads with the function LoadMappedReads()  
加载映射得到的数据框结构读取与功能LoadMappedReads（）


参数：sample
data.frame structure obtained by loading the mapped reads with the function LoadMappedReads()
加载映射得到的数据框结构读取与功能LoadMappedReads（）


参数：fileOutput
Name of the file were the results will be written  
的文件名的结果将被写入


参数：chr
Character vector containing the chromosome names as identified on q.
特征向量包含确定q染色体的名字。


参数：chrL
Numeric vector containing the length (bp) of the chromosomes. It should be in the same order than chr  
数字向量，染色体的长度（BP）。它应该是在相同的顺序比chr


参数：w
Integer corresponding to the desired length of the extended reads.   
扩展到所需长度的整数，对应读取。


参数：considerStrand
Character value.  "Minimum"=>Default value. Report the minimum number of hits at each nucleotide position for both strands.  "Foward"=> Report the number of hits at each nucleotide position for the "foward" strands (the one denoted as "+" in q).  "Reverse"=>Report the number of hits at each nucleotide position for the "reverse" strands (the one denoted as "-" in q).   "Sum"=>Report the sum of number of hits at each nucleotide position for both strands.  
字符值。 “最低”=>“默认值”。报告每两股核苷酸位置命中的最低数量。 “转寄友人”=>报告“转寄友人”链的每个核苷酸位置的点击数（表示在q的为“+”）。 “反向”=>报告为“反向”链的每个核苷酸位置的点击数（表示一个“ - ”q的）。 “心”=>报告每两股核苷酸位置的点击次数的总和。


参数：uniquelyMapped
  Logic value, If TRUE, only consider unquely mapped reads.  
逻辑值，如果为TRUE，只考虑unquely映射读取。


参数：uniquePosition
Logic value. If TRUE, only consider reads mapped in different positions.  
逻辑值。如果是TRUE，只考虑在不同的位置读取映射。


参数：norm
Integer value. Number of hits will be reported by number of hits per norm nucleotides  
整数值。命中每norm核苷酸的数量，将报告的点击次数


参数：backg
Any region with a hit value lower than backg in the control will be set to the value of backg  
任何一击值较低的区域比backg在control将设置的的backg价值


参数：t
Numeric value. Read-enriched regions are calculated as genomic regions with score values bigger than t   
数值。读富集区域计算基因组区域的分值比t大


参数：g
Integer value. The maximum gap allowed between regions. Regions that are less than g bps away will be merged.  
整数值。区域之间允许的最大差距。区域的少比g基点的距离将被合并。


参数：times
To be memory efficient, CSAR will only upload to the RAM memory fragments of length times. A bigger value means more RAM memory needed but whole process will be faster
到内存效率的CSAR只会上传到RAM内存片断长度times。一个更大的值意味着需要更多的RAM内存，但整个过程会更快


参数：digits
Number of decimal digits used to report the score values
报告得分值的小数位数数目


参数：test
Use a score based on the poisson distribution ("Poisson") or in the ratio ("Ratio")  
使用泊松分布（泊松）的比例为基础的得分（“比”）


Details

详情----------Details----------

The parameter values should be the same than the one used in sigWin, ChIPseqScore, and mappedReads2Nhits. The label "control" and "sample" is asigned to each read to identify from which group they came. Labels are randomly permutated, and read-enriched regions for this new permuated dataset are calculated.
参数值应该比一个sigWin，ChIPseqScore，mappedReads2Nhits相同。标签“控制”和“样本”asigned每个读，以确定他们来到哪个组。标签随机permutated，计算本的新permuated集读丰富的区域。


值----------Value----------

The file filePutput is created with the next columns:
filePutput下一列创建文件：


参数：chr
Chromosome name
染色体的名字


参数：start
Start of the read-enriched region
开始读富集区域


参数：end
End of the read-enriched region
读富集区域结束


参数：posPeak
Position of the maximum score value on the read-enriched region
读富集区域的最高得分值的位置


参数：score
Maximum score value on the read-enriched region
读富集区域的最高得分值


参数：length
Read-enriched region length
读富集区的长度


作者（S）----------Author(s)----------


Jose M Muino, <a href="mailto:jose.muino@wur.nl">jose.muino@wur.nl</a>



参考文献----------References----------



参见----------See Also----------

CSAR-package,getPermutatedWinScores
的CSAR-包，getPermutatedWinScores


举例----------Examples----------



##For this example we will use the a subset of the SEP3 ChIP-seq data (Kaufmann, 2009)[＃在这个例子中，我们将使用的SEP3的ChIP-seq的数据的一个子集（考夫曼，2009）]
data("CSAR-dataset");
##We calculate the number of hits for each nucleotide posotion for the control and sample. We do that just for chromosome chr1, and for positions 1 to 10kb[＃我们计算每个核苷酸posotion为控制和样品的点击次数。我们只是做染色体chr1的职位1到10KB]
nhitsS<-mappedReads2Nhits(sampleSEP3_test,file="sampleSEP3_test",chr=c("CHR1v01212004"),chrL=c(10000))
nhitsC<-mappedReads2Nhits(controlSEP3_test,file="controlSEP3_test",chr=c("CHR1v01212004"),chrL=c(10000))


##We calculate two sets of read-enrichment scores through permutation[＃我们计算通过置换两种套读富集分数]
permutatedWinScores(nn=1,sample=sampleSEP3_test,control=controlSEP3_test,fileOutput="test",chr=c("CHR1v01212004"),chrL=c(100000))
permutatedWinScores(nn=2,sample=sampleSEP3_test,control=controlSEP3_test,fileOutput="test",chr=c("CHR1v01212004"),chrL=c(100000))


转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


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